WormBase-Caltech Weekly Calls December 2016

December 1, 2016

Micropublication grant

• Daniela and Karen working on
• Pulled out papers that mention "unpublished" and "data not shown"
• Working with Transgenome project and GSA
• Deadline Dec 15th
• Proposal for BD2K call, multiple agencies (NHGRI)
• Focusing on curation process (as opposed to publication process)
• Have "unpublished" data mentioned in one paper later published in another? Maybe, difficult to know
• Could sample ~20 papers to check
• Another approach could check how many chapters from PhD theses are unpublished
• Could ask authors (source of personal communication) if they've ever published the data
• Check BioArchive, how much is still unpublished 5 years out?
• Could be a process where authors cannot say "data not shown" they need to micropublish
• Any published reports about how much unpublished data there is?
• What are the numbers for fly, mouse (other organism) papers?
• Micropublications are something that AGR is interested in

GoToMeeting trial

• Allows computer call-in or phone dial in
• Reasonably priced, but costs add up if many people are dialing in with the toll-free number (8 cents per minute per person)
• Allows for multiple webcams and screen sharing
• People generally like it

Citace upload

• January 13th, 2017

December 8, 2016

LinkOut from PubMed paper pages to WormBase paper pages?

• GO recently established link outs from PubMed to AmiGO
• TAIR links out from PubMed to TAIR paper pages
• Do this for WB (and AGR)?
• Can take a look at WB paper pages, maybe clean up, e.g. make less jargony

AGR meeting

• Faceted search for data across MODs
• Goal: Common gene report page
  • Minimal gene report page by March
    • gene id, names
    • gene concise description
    • gene sequences
    • gene location/structure
    • gene orthology
    • gene-disease connections
    • gene ontology (go-slim ribbons)
• AGR use case meeting yesterday discussed outcome of Denver meeting
  • Figuring out the role of the use case working group with new working groups
• GO slims - generic or organism-specific? Possibly both; we should see what works
• Project manager? Maybe
• Gene descriptions
  • ZFIN doesn't have them; could we take advantage of automated descriptions?

WormBase grant

• Need to submit in May or September
• What needs to be thought about for the renewal?
  • Datomic will continue (should be done by new grant cycle)
  • Curation
    • What's happening in community annotation?
      • We can use existing phenotype pipeline
      • Can encourage bulk data uploads
    • What data are we curating?
    • Noctua training and implementation
    • Disease curation becoming standard
    • Molecule curation
    • Physical interaction curation: most DBs farm out; we do our own
      • Common, basic datatype that could be curated by international curation efforts
    • Pathway curation
      • Can we establish automated pipelines to pull in pathway annotations from core data?

SObA graphs for gene ontology data

• Raymond & Juancarlos will work on a SObA graph for GO annotations
• Similar to existing phenotype graph, e.g.: http://www.wormbase.org/species/c_elegans/gene/WBGene00006763#b--10

December 15, 2016

AGR use case working group

• Members of use case WG will be delegated to smaller working groups to help build the AGR portal gene report page
• Chris working with disease working group to build a disease widget on a gene report page

SObA graphs for gene ontology data

• Raymond and Juancarlos are working on it
• Have contacted Chris Mungall for advice

Gene enrichment analysis

• Raymond working with David Angeles to create more enrichment analysis tools
• To include GO term and phenotype enrichment analysis (hyper-geometric test)